[Bioc-devel] as.character method for GenomicRanges?

On 04/24/2015 11:41 AM, Michael Lawrence wrote:

Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a
count mcol. Should be easy to support but what should the API be like?

This was actually the motivating use case for introducing
findMatches/countMatches a couple of years ago:

  ux <- unique(x)
  mcols(ux)$Freq <- countMatches(ux, x)

Don't know what a good API would be to make this even more
straightforward though. Maybe via some extra argument to unique()
e.g. 'with.freq'? This is kind of similar to the 'with.revmap'
argument of reduce(). Note that unique() could also support the
'with.revmap' arg. Once it does, the 'with.freq' arg can also
be implemented by just calling elementLengths() on the "revmap"
metadata column.

H.

On Fri, Apr 24, 2015 at 10:54 AM, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org>> wrote:

    On 04/24/2015 10:18 AM, Michael Lawrence wrote:

        It is a great idea, but I'm not sure I would use it to implement
        table(). Allocating those strings will be costly. Don't we
        already have
        the 4-way int hash? Of course, my intuition might be completely
        off here.


    It does use the 4-way int hash internally. as.character() is only used
    at the very-end to stick the names on the returned table object.

    H.



        On Fri, Apr 24, 2015 at 9:59 AM, Herv? Pag?s
        <hpages at fredhutch.org <mailto:hpages at fredhutch.org>
        <mailto:hpages at fredhutch.org <mailto:hpages at fredhutch.org>>>
wrote:

             Hi Pete,

             Excellent idea. That will make things like table() work
        out-of-the-box
             on GenomicRanges objects. I'll add that.

             Thanks,
             H.



             On 04/24/2015 09:43 AM, Peter Haverty wrote:

                 Would people be interested in having this:

                 setMethod("as.character", "GenomicRanges",
                             function(x) {
                                 paste0(seqnames(x), ":", start(x), "-",
        end(x))
                             })

                 ?

                 I find myself doing that a lot to make unique names or
for
                 output that
                 goes to collaborators.  I suppose we might want to tack
        on the
                 strand if it
                 isn't "*".  I have some code for going the other
        direction too,
                 if there is
                 interest.



                 Pete

--
Herv? Pag?s

Program in Computational Biology
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